Gut metagenome in FMT for recurrent C. difficile, Canada
83 stool metagenome samples from Canada, from patients with recurrent C. difficile infection/diarrhoea and their fecal microbiota transplant donors, in a case-control study of FMT success. machine-written summary
83 samples · 83 runs · CA · Age unknown · 2018 · 26.4 Mbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 746 sample values (collection date, country, health condition, health condition detail, intervention, intervention detail, latitude, location region) |
| ✓ Abstract / description | 96 sample values (health condition, health condition detail) |
| ○ Full text | read; no usable statement or table · PMC10311314, PMC6867182 |
| ✓ Supplementary tables | 26 sample values (subject id) |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
intervention · arms resolved
19 people have samples in more than one arm.
Faecal microbiota transplantation design single_arm_before_after · population gi_infection_or_diarrhoea · FMT via colonoscopy for recurrent C. difficile infection
“received FMT from volunteer donors” — abstract:30866714 (study level; per-sample arms are in the intervention column below)
longitudinalFMT donor → recipient
23 of 27 people sampled more than once (79 samples; median 3, up to 12 per person) · follow-up median 46 d (max 19 mo) · median interval between samples 21 d (time from collection dates). Schedule stated by the source: “Patients sampled before FMT and after FMT (early/late), some after a 2nd FMT (early/late); donors sampled once or more as linked donor stool.” (time origin: FMT).
Each row is one person (23 shown); dots are samples at days since that person's first sample.
FMT for rCDI: 26 donor stool samples from 7 donors linked to their recipients (donor_of relations, 19 recipients).
donorrecipient · circles are people (pale = no sequenced sample), arrows run donor → recipient and parent → child, curved lines join twins, partners and siblings, squares are shared settings or families without recorded roles. Shown: 4 linked groups from explicit relations. 27 people in the project overall.
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 0 | 0% | ||||
| country | 83 | 100% | 83 | |||
| health_condition | 83 | 100% | 44 | 39 | ||
| subject_id | 83 | 100% | 57 | 26 | ||
| collection_date | 83 | 100% | 83 | |||
| detailed_location | 83 | 100% | ||||
| health_condition_detail | 83 | 100% | 26 | 57 | ||
| intervention | 83 | 100% | 83 | |||
| intervention_detail | 83 | 100% | 83 | |||
| latitude | 83 | 100% | 83 | |||
| location_region | 83 | 100% | 83 | |||
| longitude | 83 | 100% | 83 | |||
| timepoint_label | 38 | 46% | 38 |
- The success of fecal microbial transplantation in Clostridium difficile infection correlates with bacteriophage relative abundance in the donor: a retrospective cohort study. 2019 PMID 30866714 PMC6867182 own_data
- Bakdrive: identifying a minimum set of bacterial species driving interactions across multiple microbial communities. 2023 PMID 37387148 PMC10311314 own_data
Archive description
Alteration of microbiome and phagenome
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.70. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site run.scientific_name · “gut metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN09060829 | collection_date | 2012-12-07 | R1 | 0.90 | biosample.attribute:collection_date | 2012-12-07 |
| SAMN09060829 | country | CA | R1 | 0.90 | sample.attr.geographic_location | Canada |
| SAMN09060841 | health_condition | healthy_control | R1 | 0.85 | biosample.attribute:description | Donor Number |
| SAMN09060887 | health_condition | gi_infection_or_diarrhoea | R1 | 0.50 | biosample_attr | 1st_FMT |
| SAMN09060829 | health_condition | gi_infection_or_diarrhoea | R4 | 0.50 | paper.abstract | Subjects with rCDI (n = 19) received FMT |
| SAMN09060841 | health_condition_detail | Donor Number | R1 | 0.85 | biosample.attribute:description | Donor Number |
| SAMN09060829 | health_condition_detail | relapsing Clostridium difficile infection | R4 | 0.50 | paper.abstract | relapsing Clostridium difficile infection (rCDI) |
| SAMN09060829 | intervention | no_intervention | R1 | 0.80 | biosample.attribute:group | group: BFT |
| SAMN09060829 | intervention_detail | baseline sample before FMT | R1 | 0.80 | biosample.attribute:group | group: BFT |
| SAMN09060829 | latitude | 53.5232 | R1 | 0.90 | biosample.attribute:latitude_and_longitude | 53.523219 N 113.526319 W |
| SAMN09060829 | location_region | Alberta | R1 | 0.60 | biosample.attribute:latitude_and_longitude | 53.523219 N 113.526319 W |
| SAMN09060829 | longitude | -113.5263 | R1 | 0.90 | biosample.attribute:latitude_and_longitude | 53.523219 N 113.526319 W |
| SAMN09060829 | subject_id | Pt0003 | R1 | 0.85 | sample.attr.patient | Pt0003 |
| SAMN09060841 | subject_id | Dr0010 | R2 | 0.80 | archive | |
| SAMN09060853 | timepoint_label | After FMT early | R1 | 0.85 | biosample.attribute:description | After FMT early |
Sequencing
83 runs over 83 samples · mean 31.5 Mbp per run (median 26.4 Mbp, total 2.62 Gbp; 83 runs with a base count) · layout PAIRED 83 · platform ILLUMINA 83 · models Illumina MiSeq (83) · 0% of runs with a Sandpiper profile · first public 2018-05-08
Authors (11)
Park H first · Laffin MR · Jovel J · Millan B · Hyun JE · Hotte N · Kao D · Madsen KL last · Wang Q first · Nute M · Treangen TJ last
Downloads
PRJNA454892.csv.gz (3.6 KB) · parquet (75.1 KB) — all 83 samples, every field with route and confidence · PRJNA454892_determinations.csv.gz (8.0 KB) — 868 evidence rows